Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB15824 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Expression analysis on the Phc1-KO neural progenitor cells
| PRJDB15810 | ENA
Project description:<p>Non-coding regions comprise most of the human genome and harbor a significant fraction of risk alleles for neuropsychiatric diseases, yet their functions remain poorly defined. We created a high-resolution map of non-coding elements involved in human cortical neurogenesis by contrasting chromatin accessibility and gene expression in the germinal zone and cortical plate of the developing cerebral cortex. To obtain a high resolution depiction of chromatin structure and gene expression in developing human fetal cortex, we dissected the post-conception week (PCW) 15-17 human neocortex into two major anatomical divisions to distinguish between proliferating neural progenitors and post mitotic neurons: (1) GZ: the neural progenitor-enriched region encompassing the ventricular zone (VZ), subventricular zone (SVZ), and intermediate zone (IZ) and (2) CP: the neuron-enriched region containing the subplate (SP), cortical plate (CP), and marginal zone (MZ). Tissues were obtained from three independent donors and three to four technical replicates from each tissue were processed for ATAC-seq to define the landscape of accessible chromatin and RNA-seq for genome-wide gene expression profiling.</p>
| phs001438 | dbGaP
Project description:Purpose: Characterization of cell types in wild-type and TCTN2 KO human neural tube organoids (hNTOs). Methods: Wild-type and TCTN2 KO hNTOs were harvested at day11. Libraries were prepared using Single Cell 3′Library & gel Bead kit v3.1 (10x Genomics, Cat# PN-1000121) according to the manufacturer’s protocol for 10000 cells recovery. Results: 13 neural progenitor cells were detected in wild-type hNTOs, and TCTN2 deficiency led to reduction of ventral progenitors cells. Conclusions: A well-organized nueral tube organoid was constructed by applying BMP and SHH morphogen gradients.
2024-02-06 | GSE254817 | GEO
Project description:Hematopoietic stem cells (HSCs) have long been the focus of developmental and regenerative studies, yet our understanding of the signaling events regulating their specification remains incomplete. We demonstrate that supt16h, a component of the FAcilitates Chromatin Transcription (FACT) complex, is required for HSC formation. Zebrafish supt16h mutants express reduced levels of Notch signaling components, genes essential for HSC development, due to abrogated transcription. Classically, Supt16h regulates transcription and nucleosome reorganization. Whereas global chromatin accessibility in supt16h mutants is unaffected, we observe a specific increase in accessibility at the p53 locus, causing an accumulation of p53 mRNA and protein. We further demonstrate that P53 levels directly influence expression of the Polycomb Group protein, phc1, which functions as a transcriptional repressor of Notch genes. Suppression of phc1 or its upstream regulator, p53, rescues both loss of Notch and loss of HSC phenotypes in supt16h mutants. Taken together, our results highlight a previously uncharacterized relationship between supt16h, p53, and phc1 to specify HSCs via modulation of Notch signaling.
2020-09-01 | GSE116088 | GEO
Project description:Haematopoietic stem cells (HSCs) have long been the focus of developmental and regenerative studies, yet our understanding of the signalling events regulating their specification remains incomplete. We demonstrate that supt16h, a component of the FAcilitates Chromatin Transcription (FACT) complex, is required for HSC formation. Zebrafish supt16h mutants express reduced levels of Notch signalling components, genes essential for HSC development, due to abrogated transcription. Classically, Supt16h regulates transcription and nucleosome reorganization. Whereas global chromatin accessibility in supt16h mutants is unaffected, we observe a specific increase in accessibility at the p53 locus, causing an accumulation of p53 mRNA and protein. We further demonstrate that P53 levels directly influence expression of the Polycomb Group protein, phc1, which functions as a transcriptional repressor of Notch genes. Suppression of phc1 or its upstream regulator, p53, rescues both loss of Notch and loss of HSC phenotypes in supt16h mutants. Taken together, our results highlight a previously uncharacterized relationship between supt16h, p53, and phc1 to specify HSCs via modulation of Notch signalling.
2020-09-01 | GSE127555 | GEO
Project description:Genome-wide chromatin state maps of murine embryonic stem (ES) cells, ES-derived neural progenitor cells and whole brain tissue. The data were generated to examine the correlation between histone and DNA methylation during lineage-commitment. Keywords: High-throughput ChIP-sequencing, Illumina, cell type comparison
2008-07-06 | GSE11172 | GEO
Project description:ATAC-Seq experiments were performed to elucidate the chromatin state changes among naïve CD4+ T cells, WT follicular helper T (TFH) cells and WT type 1 helper T (TH1) cells Day2 (D2), Day5 (D5), Day8 (D8) post-LCMV-Armstrong infection, as well as EZH2-null (KO) TFH and TH1 at Day8 post-LCMV-infection. The analysis suggested stringent lineage-specific mode of chromatin accessibility in each group, indicating chromatin remodeling is tightly associated with TFH versus TH1 lineage differentiation in response to acute viral infection. Furthermore, the comparison between wild-type and EZH2-null TFH cells showed that less-opening state of certain chromatin accessible region in TFH-differentiation associated genes in the formers, suggesting EZH2 led to permissive chromatin accessibility primarily at specific regions of TFH-associated genes. H3K27me3-ChIP-seq was performed in WT TFH and TH1 cells to confirm the deposition of the histone marks at those loci.
2018-12-31 | GSE120532 | GEO
Project description:Comparison of gene expression between wild type and AP2-L KO parasites
| PRJNA156269 | ENA
Project description:Comparison of gene expression between wild type and AP2-G KO parasites.
| PRJNA156295 | ENA
Project description:Comparison of gene expression between Ftx KO eyes and wild type eyes
| PRJNA392685 | ENA